Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010521.1 Corchorus capsularis cultivar CVL-1 contig10542, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 36159
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:790 original size:322 final size:323
Alignment explanation
Indices: 1--1464 Score: 1643
Period size: 322 Copynumber: 4.5 Consensus size: 323
* * * * *
1 AGATGCTCGTAAAAACAAATCGTTATATCCGATGTCGCTGGAATTTGGTTCGATGAATATAAGTA
1 AGATGCTCGTAAAAACAAATCGTTAAATCCAATGTGGCTGGAATTTGGTTCGATAAATATAAATA
* * * *
66 TCTCAAGGAGTCTTTACGCCAAAAATAATGCAAACCTAAGCCGGCG-CCCAAAATGCGTTTTTAG
66 TTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGCGCCCCAAAATGCGTTTTTAG
** * * * *
130 CCAAAAATTGTGATGGTTGGTACACGATTTCGGCTAAAAACTGACCAGAAAAATTTTTTTCTAAA
131 CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCGGAAGAATTTTTTTCTCAA
** *
195 TTTTTTGCTACAATACGAATAAAAAATATATAATTCAACTCCAAAAAGATTAAAGGGTTTTTCAC
196 TTTTTTGCTACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGGTTTTTCAC
* *
260 GCTTCTAATATCGTTTTTC-CATTTTTTTTCCGAATTAATTTCTAATCAAATCGAAATAACATTC
261 GCTTCTAATATCGTTTTTCACA--TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAACATTC
* *
324 AGATGCTCGTAAAAACAAATCGTTAAATCCAAAT-TGGCTGGAATTTGATTCGATGAATATAAAT
1 AGATGCTCGTAAAAACAAATCGTTAAATCC-AATGTGGCTGGAATTTGGTTCGATAAATATAAAT
** * * *
388 ATTTCAAGGAGTCCATACGCAAAAAATCATACAAACCTGAGCCGGCGCCCCAAAATGCGTTTTTA
65 ATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGCGCCCCAAAATGCGTTTTTA
* *
453 GCCCAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCGGAAGAATTTTTTTCTCA
130 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCGGAAGAATTTTTTTCTCA
*
518 ATTTTTTGCTACAATACTCATAAAAAATATATAATTCAACTCCAAAAAGATTAAAGGGTTTTTCA
195 ATTTTTTGCTACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGGTTTTTCA
* *
583 CGCTTCTAATATCGTGTTTC-CATTTTTTCCGAATTAATTTCTAATTAAATCGAAATAACATTC
260 CGCTTCTAATATCGTTTTTCACATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAACATTC
* *
646 AGATGCTCGTAAAAACAAATCGTTAAATCCAAAT-TGGTTGGAATTTGGTTCAATAAATATAAAT
1 AGATGCTCGTAAAAACAAATCGTTAAATCC-AATGTGGCTGGAATTTGGTTCGATAAATATAAAT
* * *
710 ATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCATAATGCGTTTTTA
65 ATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGCGCCCCAAAATGCGTTTTTA
* ** ** *
775 GCCAAAAACCGTGAT-G--AGTAAACGATTTCGGCTAAAATTTTGCAAAAGCTAAGGGGAAATTT
130 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA-ACTG--ACCG-GAA---G-AA-TT
* * * * * * ***
837 TTTTTTTACAATTCTTTGCCACAATACTCAGAAAAAGTATATAATTCAACGCCAAAAAAATTGTT
186 TTTTTCT-CAATTTTTTGCTACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTAAA
*** *
902 GGGTTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTCCGAATTTATTTCTAATTAAATCGAA
250 GGGTTTTTCACGCTTCTAATATCGTTTTTCACATTTTTTCCGAATTAATTTCTAATTAAATCGAA
*
967 ACAAGATTC
315 ACAACATTC
* * * * * *
976 AGATGCTCGTAAAAACAAATTGTTAAATCCATTGTGG-TTGAGATTTGGTTAGATAACTATAGAT
1 AGATGCTCGTAAAAACAAATCGTTAAATCCAATGTGGCTGGA-ATTTGGTTCGATAAATATAAAT
* * * * * *
1040 ATTTTAAGGAGTC-TTACTGCCAAAAATCATGCAAAACTGAGCCAGAGCTCCGAAACGCGTTTTT
65 ATTTCAAGGAGTCTTTAC-GCCAAAAATCATGCAAAACTGAGCCGGCGCCCCAAAATGCGTTTTT
* * * * * * *
1104 AGCCAATAACCGTAATGGGTTAGTGCACGATCTGGGCTAAAAACTGACCCGAA-AA-GTTTTTCT
129 AGCCAAAAACCGTGAT-GGTTAGTACACGATTTCGGCTAAAAACTGACCGGAAGAATTTTTTTCT
* * * * *
1167 CAATTTTTTTGC-AAAATA-TTA-AAAAAATATACATAATTTAACGCCAAAAA-ATTGACGGGTT
193 CAA-TTTTTTGCTACAATACTCATAAAAAATAT--ATAATTCAACGCCAAAAAGATTAAAGGGTT
* * * * *
1228 TTTCACGCTTTTAATATCGTTTTTTCAAATTTTTTCTGAAGTAATTTATAATTAAATCGAAACAA
255 TTTCACGCTTCTAATATCG-TTTTTCACATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
*
1293 GATTC
319 CATTC
** * * * *
1298 AGATGCT--TGCAAACGAATCCTTATATCCAATGTGGCT-GAGATTTGGTTCGATAAATATAGAT
1 AGATGCTCGTAAAAACAAATCGTTAAATCCAATGTGGCTGGA-ATTTGGTTCGATAAATATAAAT
* * * * * * * * * ** * *
1360 ATTTCGAGGAGTCTCTGCGCCAAAAGTCATGTAAAATTGAGTCGGGGCTCCGGAACGTGTTTTTA
65 ATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGCGCCCCAAAATGCGTTTTTA
1425 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
130 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
1465 TTTTGCAAAA
Statistics
Matches: 987, Mismatches: 128, Indels: 56
0.84 0.11 0.05
Matches are distributed among these distances:
319 42 0.04
320 117 0.12
321 33 0.03
322 247 0.25
323 111 0.11
324 162 0.16
325 2 0.00
326 1 0.00
327 2 0.00
328 8 0.01
329 86 0.09
330 155 0.16
331 1 0.00
332 1 0.00
333 2 0.00
334 17 0.02
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (323 bp):
AGATGCTCGTAAAAACAAATCGTTAAATCCAATGTGGCTGGAATTTGGTTCGATAAATATAAATA
TTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGCGCCCCAAAATGCGTTTTTAG
CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCGGAAGAATTTTTTTCTCAA
TTTTTTGCTACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGGTTTTTCAC
GCTTCTAATATCGTTTTTCACATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAACATTC
Found at i:1262 original size:652 final size:647
Alignment explanation
Indices: 1--1474 Score: 1750
Period size: 652 Copynumber: 2.3 Consensus size: 647
* * * *
1 AGATGCTCGTAAAAACAAATCGTTATATCCGATGTCGCTGGAATTTGGTTCGATGAATATAAGTA
1 AGATGCTCGTAAAAACAAATCGTTATATCCAATGTGGCTGGAATTTGGTTCGATAAATATAAATA
* * * * * *
66 TCTCAAGGAGTCTTTACGCCAAAAATAATGCAAACCTAAGCCGGCG-CCCAAAATGCGTTTTTAG
66 TTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCAAAATGCGTTTTTAG
** * ** **
130 CCAAAAATTGTGATGGTTGGTACACGATTTCGGCTAAAA-ACTG-ACCAGAAAAATTTTTTTCTA
131 CCAAAAACCGTGATGG-TAGTACACGATTTCGGCTAAAATTTTGCAAAAGAAAAATTTTTTTCTA
* * * * *
193 AATTTTTTGCTACAATACGAATAAAAAATATATAATTCAACTCCAAAAAGATTAAAGGGTTTTTC
195 AATTCTTTGCCACAATACGAAGAAAAAATATATAATTCAACGCCAAAAAAATTAAAGGGTTTTTC
*
258 ACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTCTAATCAAATCGAAATAACATT
260 ACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTCTAATCAAATCGAAACAACATT
*
323 CAGATGCTCGTAAAAACAAATCGTTAAATCCAAATTGGCTGGAATTTGATTCGATGAATATAAAT
325 CAGATGCTCGTAAAAACAAATCGTTAAATCCAAATTGGCTGGAATTTGATTAGATGAATATAAAT
* * * *
388 ATTTCAAGGAGTCCATACGCAAAAAATCATACAAACCTGAGCCGGCGCCCCAAAATGCGTTTTTA
390 ATTTCAAGGAGTCCATACGCAAAAAATCATACAAAACTGAGCCAGAGCCCCAAAACGCGTTTTTA
* * * * *
453 GCCCAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCGGAAGAATTTTTTTCTCA
455 GCCCAAAACCGTAATGGTTAGTACACGATCTCGGCTAAAAACTGACCCGAAGAATGTTTTTCTCA
* *
518 ATTTTTTGCTACAATACTCATAAAAAATATATAATTCAACTCCAAAAAGATTAAAGGGTTTTTCA
520 ATTTTTTGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGGTTTTTCA
* * * *
583 CGCTTCTAATATCGTGTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAATAACATTC
585 CGCTTCTAATATCGTGTTTCAATTTTTTCCGAAGTAATTTATAATTAAATCGAAACAACATTC
* * *
646 AGATGCTCGTAAAAACAAATCGTTAAATCCAAAT-TGGTTGGAATTTGGTTCAATAAATATAAAT
1 AGATGCTCGTAAAAACAAATCGTTATATCC-AATGTGGCTGGAATTTGGTTCGATAAATATAAAT
*
710 ATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCATAATGCGTTTTTA
65 ATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCAAAATGCGTTTTTA
*
775 GCCAAAAACCGTGAT-G-AGTAAACGATTTCGGCTAAAATTTTGCAAAAGCTAAGGGGAAATTTT
130 GCCAAAAACCGTGATGGTAGTACACGATTTCGGCTAAAATTTTGCAAAAG--AA----AAA-TTT
* ** * ***
838 TTTTTTACAATTCTTTGCCACAATACTCAGAAAAAGTATATAATTCAACGCCAAAAAAATTGTTG
188 TTTTCTA-AATTCTTTGCCACAATACGAAGAAAAAATATATAATTCAACGCCAAAAAAATTAAAG
* * *
903 GGTTTTTCACGCTTCTAATATCGTTTTT-CTTTTTTTTTCCGAATTTATTTCTAATTAAATCGAA
252 GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTCTAATCAAATCGAA
* * * * *
967 ACAAGATTCAGATGCTCGTAAAAACAAATTGTTAAATCC--ATTGTGGTTGAGATTTGGTTAGAT
317 ACAACATTCAGATGCTCGTAAAAACAAATCGTTAAATCCAAATTG-GCTGGA-ATTTGATTAGAT
* * * * * * *
1030 -AACTATAGATATTTTAAGGAGT-CTTACTGCCAAAAATCATGCAAAACTGAGCCAGAGCTCCGA
380 GAA-TATAAATATTTCAAGGAGTCCATAC-GCAAAAAATCATACAAAACTGAGCCAGAGCCCCAA
* *
1093 AACGCGTTTTTAG-CCAATAACCGTAATGGGTTAGTGCACGATCTGGGCTAAAAACTGACCCGAA
443 AACGCGTTTTTAGCCCAA-AACCGTAAT-GGTTAGTACACGATCTCGGCTAAAAACTGACCCGAA
* *
1157 -AA-GTTTTTCTCAATTTTTTTGC-AAAATA-TTA-AAAAAATATACATAATTTAACGCCAAAAA
506 GAATGTTTTTCTCAA-TTTTTTGCTAAAATACTCATAAAAAATAT--ATAATTCAACGCCAAAAA
* * * * *
1217 -ATTGACGGGTTTTTCACGCTTTTAATATCGTTTTTTCAAATTTTTTCTGAAGTAATTTATAATT
568 GATTAAAGGGTTTTTCACGCTTCTAATATCG-TGTTTC-AATTTTTTCCGAAGTAATTTATAATT
*
1281 AAATCGAAACAAGATTC
631 AAATCGAAACAACATTC
** * * *
1298 AGATGCT--TGCAAACGAATCCTTATATCCAATGTGGCT-GAGATTTGGTTCGATAAATATAGAT
1 AGATGCTCGTAAAAACAAATCGTTATATCCAATGTGGCTGGA-ATTTGGTTCGATAAATATAAAT
* * * * * * * ** * *
1360 ATTTCGAGGAGTCTCTGCGCCAAAAGTCATGTAAAATTGAG-TCGGGGCTCCGGAACGTGTTTTT
65 ATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCT-GGGGCCCCAAAATGCGTTTTT
1424 AGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAA
129 AGCCAAAAACCGTGATGG-TAGTACACGATTTCGGCTAAAATTTTGCAAAA
1475 ACAAATCCGT
Statistics
Matches: 704, Mismatches: 96, Indels: 50
0.83 0.11 0.06
Matches are distributed among these distances:
643 19 0.03
644 2 0.00
645 99 0.14
646 31 0.04
647 2 0.00
649 15 0.02
650 140 0.20
651 54 0.08
652 206 0.29
653 136 0.19
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (647 bp):
AGATGCTCGTAAAAACAAATCGTTATATCCAATGTGGCTGGAATTTGGTTCGATAAATATAAATA
TTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCAAAATGCGTTTTTAG
CCAAAAACCGTGATGGTAGTACACGATTTCGGCTAAAATTTTGCAAAAGAAAAATTTTTTTCTAA
ATTCTTTGCCACAATACGAAGAAAAAATATATAATTCAACGCCAAAAAAATTAAAGGGTTTTTCA
CGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTCTAATCAAATCGAAACAACATTC
AGATGCTCGTAAAAACAAATCGTTAAATCCAAATTGGCTGGAATTTGATTAGATGAATATAAATA
TTTCAAGGAGTCCATACGCAAAAAATCATACAAAACTGAGCCAGAGCCCCAAAACGCGTTTTTAG
CCCAAAACCGTAATGGTTAGTACACGATCTCGGCTAAAAACTGACCCGAAGAATGTTTTTCTCAA
TTTTTTGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGGTTTTTCAC
GCTTCTAATATCGTGTTTCAATTTTTTCCGAAGTAATTTATAATTAAATCGAAACAACATTC
Found at i:10696 original size:21 final size:21
Alignment explanation
Indices: 10670--10709 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
10660 ATTTCTAATA
10670 AATAAATTGAGAAATAGATCT
1 AATAAATTGAGAAATAGATCT
10691 AATAAATTGAGAAATAGAT
1 AATAAATTGAGAAATAGAT
10710 ACTAGAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.15, T:0.28
Consensus pattern (21 bp):
AATAAATTGAGAAATAGATCT
Found at i:10712 original size:104 final size:105
Alignment explanation
Indices: 10584--10792 Score: 393
Period size: 105 Copynumber: 2.0 Consensus size: 105
10574 TGTTTAATGT
*
10584 TCTAATAAATTGAGAAATAGATACTAGAATGTTATTTTGGAAAATTTCC-TCTTTTTTTTTTGAA
1 TCTAATAAATTGAGAAATAGATACTAGAATGTTATTTTGGAAAATTTCCTTCTTTTTTTTTGGAA
*
10648 AGAAATGTTTAAATTTCTAATAAATAAATTGAGAAATAGA
66 AAAAATGTTTAAATTTCTAATAAATAAATTGAGAAATAGA
10688 TCTAATAAATTGAGAAATAGATACTAGAATGTTATTTTGGAAAATTTCCTTCTTTTTTTTTGGAA
1 TCTAATAAATTGAGAAATAGATACTAGAATGTTATTTTGGAAAATTTCCTTCTTTTTTTTTGGAA
10753 AAAAATGTTTAAATTTCTAATAAATAAATTGAGAAATAGA
66 AAAAATGTTTAAATTTCTAATAAATAAATTGAGAAATAGA
10793 AATGTACTAC
Statistics
Matches: 102, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
104 49 0.48
105 53 0.52
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (105 bp):
TCTAATAAATTGAGAAATAGATACTAGAATGTTATTTTGGAAAATTTCCTTCTTTTTTTTTGGAA
AAAAATGTTTAAATTTCTAATAAATAAATTGAGAAATAGA
Found at i:11925 original size:43 final size:43
Alignment explanation
Indices: 11845--11927 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
11835 AACCGTTTCA
* **
11845 GAAGCAATGGCAAACAATTGCTCTGCACATTACGATTAAAAAT
1 GAAGCAATGGCAAACAATTGCTCAGCACAAAACGATTAAAAAT
*
11888 GAAGCAATGGCAAACAATTGCTCAGCACAAAATGATTAAA
1 GAAGCAATGGCAAACAATTGCTCAGCACAAAACGATTAAA
11928 TATAAGACAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (43 bp):
GAAGCAATGGCAAACAATTGCTCAGCACAAAACGATTAAAAAT
Found at i:15411 original size:14 final size:15
Alignment explanation
Indices: 15392--15422 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
15382 GCCGTGTGTG
15392 TTGAAAG-TTGAAAC
1 TTGAAAGTTTGAAAC
15406 TTGAAAGTTTGAAAC
1 TTGAAAGTTTGAAAC
15421 TT
1 TT
15423 CTTCCCGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (15 bp):
TTGAAAGTTTGAAAC
Found at i:15853 original size:16 final size:16
Alignment explanation
Indices: 15832--15864 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
15822 CAAACAAACT
15832 TAAAATTTTCGAGATC
1 TAAAATTTTCGAGATC
15848 TAAAATTTTCGAGATC
1 TAAAATTTTCGAGATC
15864 T
1 T
15865 GATCCTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (16 bp):
TAAAATTTTCGAGATC
Found at i:15969 original size:36 final size:36
Alignment explanation
Indices: 15920--15995 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
15910 CGCCTGCTGT
*
15920 CGCTTCTTTGAGTACTGCTCCTTCAACTTCTTCCGC
1 CGCTTCTTCGAGTACTGCTCCTTCAACTTCTTCCGC
*
15956 CGCTTCTTCGAGTACTGCTCCTTCAACTTCTTTCGC
1 CGCTTCTTCGAGTACTGCTCCTTCAACTTCTTCCGC
15992 CGCT
1 CGCT
15996 ATTGACACCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.11, C:0.37, G:0.14, T:0.38
Consensus pattern (36 bp):
CGCTTCTTCGAGTACTGCTCCTTCAACTTCTTCCGC
Found at i:17704 original size:27 final size:27
Alignment explanation
Indices: 17666--17719 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
17656 TTTCACAACA
17666 AAATTTCATTTCTTAACTGAATTTTCT
1 AAATTTCATTTCTTAACTGAATTTTCT
17693 AAATTTCATTTCTTAACTGAATTTTCT
1 AAATTTCATTTCTTAACTGAATTTTCT
17720 TAAAAGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.52
Consensus pattern (27 bp):
AAATTTCATTTCTTAACTGAATTTTCT
Found at i:17718 original size:14 final size:14
Alignment explanation
Indices: 17674--17722 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
17664 CAAAATTTCA
17674 TTTCTTAACTGAAT
1 TTTCTTAACTGAAT
* * **
17688 TTTCTAAATTTCA-
1 TTTCTTAACTGAAT
17701 TTTCTTAACTGAAT
1 TTTCTTAACTGAAT
17715 TTTCTTAA
1 TTTCTTAA
17723 AAGAATTTAT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (14 bp):
TTTCTTAACTGAAT
Found at i:17730 original size:27 final size:27
Alignment explanation
Indices: 17673--17730 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
17663 ACAAAATTTC
***
17673 ATTTCTTAACTGAATTTTCTAAATTTC
1 ATTTCTTAACTGAATTTTCTAAATAGA
17700 ATTTCTTAACTGAATTTTCTTAAA-AGA
1 ATTTCTTAACTGAATTTTC-TAAATAGA
17727 ATTT
1 ATTT
17731 ATAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (27 bp):
ATTTCTTAACTGAATTTTCTAAATAGA
Found at i:19695 original size:92 final size:92
Alignment explanation
Indices: 19538--19721 Score: 314
Period size: 92 Copynumber: 2.0 Consensus size: 92
19528 GGTTATGTCT
* * *
19538 GGCTTAGTGTGGTAGGGTGAGTCCGGACATCCGGCAATGCTTCTGCAGAGGGTTATGGCATATGA
1 GGCTTAGTGTGGTAGGATGAGTCCAGACATCCGGCAATGCTTCTACAGAGGGTTATGGCATATGA
*
19603 CTAATTAACAAATTGATAGGGAGAAGC
66 CTAATGAACAAATTGATAGGGAGAAGC
*
19630 GGCTTAGTGTGGTAGGATGAGTCCAGACATCCGGTAATGCTTCTACAGAGGGTTATGGCATATGA
1 GGCTTAGTGTGGTAGGATGAGTCCAGACATCCGGCAATGCTTCTACAGAGGGTTATGGCATATGA
*
19695 CTAATGAACAAATTGATGGGGAGAAGC
66 CTAATGAACAAATTGATAGGGAGAAGC
19722 AAGCGTTTTC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 86 1.00
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (92 bp):
GGCTTAGTGTGGTAGGATGAGTCCAGACATCCGGCAATGCTTCTACAGAGGGTTATGGCATATGA
CTAATGAACAAATTGATAGGGAGAAGC
Found at i:21154 original size:25 final size:26
Alignment explanation
Indices: 21126--21176 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
21116 AAGTAATGTA
21126 TGAAC-AAATTTTGTAGTACAGTATT
1 TGAACAAAATTTTGTAGTACAGTATT
*
21151 TGAACAAAAAATTTTGTTGTACAGTA
1 TGAAC--AAAATTTTGTAGTACAGTA
21177 AAGAGGATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
28 17 0.77
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (26 bp):
TGAACAAAATTTTGTAGTACAGTATT
Found at i:26429 original size:50 final size:50
Alignment explanation
Indices: 26357--26456 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
26347 GAAATGCTTA
26357 TTTTGAATATCCAGTCCTTATAAGCTGAGATTCCATTCTACTTAGCATAT
1 TTTTGAATATCCAGTCCTTATAAGCTGAGATTCCATTCTACTTAGCATAT
26407 TTTTGAATATCCAGTCCTTATAAGCTGAGATTCCATTCTACTTAGCATAT
1 TTTTGAATATCCAGTCCTTATAAGCTGAGATTCCATTCTACTTAGCATAT
26457 ACATTTAATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (50 bp):
TTTTGAATATCCAGTCCTTATAAGCTGAGATTCCATTCTACTTAGCATAT
Found at i:30342 original size:30 final size:30
Alignment explanation
Indices: 30306--30378 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
30296 CGATGCCTAA
*
30306 TTCAGTGTTGACGAGGTTTAGATCGGTAGG
1 TTCAGTGTTGACGAGGGTTAGATCGGTAGG
*
30336 TTCAGTGTTGACGAGGGTTAGATCGGTATG
1 TTCAGTGTTGACGAGGGTTAGATCGGTAGG
30366 TTCAGTGTTGACG
1 TTCAGTGTTGACG
30379 TCATGCTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.19, C:0.11, G:0.36, T:0.34
Consensus pattern (30 bp):
TTCAGTGTTGACGAGGGTTAGATCGGTAGG
Found at i:33164 original size:33 final size:33
Alignment explanation
Indices: 33122--33184 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
33112 GATGACACGT
*
33122 GCCGCCCCAG-GAGGGCGGCTTACCATGGCTCAA
1 GCCGCCCCAGTG-GGGAGGCTTACCATGGCTCAA
33155 GCCGCCCCAGTGGGGAGGCTTACCATGGCT
1 GCCGCCCCAGTGGGGAGGCTTACCATGGCT
33185 TCTAGGGCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.16, C:0.35, G:0.35, T:0.14
Consensus pattern (33 bp):
GCCGCCCCAGTGGGGAGGCTTACCATGGCTCAA
Done.